<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
  <parent>
    <artifactId>phenol</artifactId>
    <groupId>org.monarchinitiative.phenol</groupId>
    <version>1.4.1</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>phenol-cli</artifactId>
  <name>phenol-cli</name>
  <description>phenol-cli gives command line access to phenol</description>
  <url>https://github.com/monarchinitiative/phenol</url>
  <build>
    <resources>
      <resource>
        <filtering>true</filtering>
        <directory>src/main/resources</directory>
      </resource>
    </resources>
    <finalName>phenol-cli</finalName>
    <plugins>
      <plugin>
        <artifactId>maven-jar-plugin</artifactId>
        <version>3.1.0</version>
        <configuration>
          <archive>
            <manifest>
              <addClasspath>true</addClasspath>
              <classpathPrefix>lib/</classpathPrefix>
              <useUniqueVersions>false</useUniqueVersions>
              <mainClass>org.monarchinitiative.phenol.cli.Main</mainClass>
            </manifest>
          </archive>
        </configuration>
      </plugin>
      <plugin>
        <artifactId>maven-shade-plugin</artifactId>
        <version>3.2.0</version>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>shade</goal>
            </goals>
            <configuration>
              <transformers>
                <transformer>
                  <mainClass>org.monarchinitiative.phenol.cli.Main</mainClass>
                </transformer>
              </transformers>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-resources-plugin</artifactId>
        <version>3.1.0</version>
        <executions>
          <execution>
            <id>copy-resources</id>
            <phase>validate</phase>
            <goals>
              <goal>copy-resources</goal>
            </goals>
            <configuration>
              <outputDirectory>${project.build.directory}/resources</outputDirectory>
              <resources>
                <resource>
                  <directory>src/resources</directory>
                  <filtering>true</filtering>
                  <includes>
                    <include>application.properties</include>
                    <include>example.settings</include>
                    <include>test.settings</include>
                    <include>log4j2.xml</include>
                  </includes>
                </resource>
              </resources>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-assembly-plugin</artifactId>
        <version>3.1.0</version>
        <executions>
          <execution>
            <id>make-assembly</id>
            <phase>package</phase>
            <goals>
              <goal>single</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
          <descriptors>
            <descriptor>src/assembly/dep.xml</descriptor>
          </descriptors>
        </configuration>
      </plugin>
    </plugins>
  </build>
  <dependencies>
    <dependency>
      <groupId>org.hamcrest</groupId>
      <artifactId>hamcrest-all</artifactId>
      <version>1.3</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.junit.jupiter</groupId>
      <artifactId>junit-jupiter-api</artifactId>
      <version>5.3.2</version>
      <scope>test</scope>
      <exclusions>
        <exclusion>
          <artifactId>apiguardian-api</artifactId>
          <groupId>org.apiguardian</groupId>
        </exclusion>
        <exclusion>
          <artifactId>opentest4j</artifactId>
          <groupId>org.opentest4j</groupId>
        </exclusion>
        <exclusion>
          <artifactId>junit-platform-commons</artifactId>
          <groupId>org.junit.platform</groupId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.junit.jupiter</groupId>
      <artifactId>junit-jupiter-params</artifactId>
      <version>5.3.2</version>
      <scope>test</scope>
      <exclusions>
        <exclusion>
          <artifactId>apiguardian-api</artifactId>
          <groupId>org.apiguardian</groupId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.junit.jupiter</groupId>
      <artifactId>junit-jupiter-engine</artifactId>
      <version>5.3.2</version>
      <scope>test</scope>
      <exclusions>
        <exclusion>
          <artifactId>junit-platform-engine</artifactId>
          <groupId>org.junit.platform</groupId>
        </exclusion>
        <exclusion>
          <artifactId>apiguardian-api</artifactId>
          <groupId>org.apiguardian</groupId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.junit-pioneer</groupId>
      <artifactId>junit-pioneer</artifactId>
      <version>0.1.2</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.mockito</groupId>
      <artifactId>mockito-core</artifactId>
      <version>2.8.47</version>
      <scope>test</scope>
      <exclusions>
        <exclusion>
          <artifactId>byte-buddy</artifactId>
          <groupId>net.bytebuddy</groupId>
        </exclusion>
        <exclusion>
          <artifactId>byte-buddy-agent</artifactId>
          <groupId>net.bytebuddy</groupId>
        </exclusion>
        <exclusion>
          <artifactId>objenesis</artifactId>
          <groupId>org.objenesis</groupId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-slf4j-impl</artifactId>
      <version>2.10.0</version>
      <scope>test</scope>
      <exclusions>
        <exclusion>
          <artifactId>log4j-api</artifactId>
          <groupId>org.apache.logging.log4j</groupId>
        </exclusion>
        <exclusion>
          <artifactId>log4j-core</artifactId>
          <groupId>org.apache.logging.log4j</groupId>
        </exclusion>
      </exclusions>
    </dependency>
  </dependencies>
  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
  </properties>
</project>
